PDBsum entry: 1peg

Transferase

PDB-id: 1peg

Biological unit* = asymmetric unit, as shown
(*as deduced by PQS)

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Description

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PROCHECK

Protein chains

266 a.a. *

Ligands

ALA-ARG-LYS-SER-THR-GLY-GLY

ALA-ARG-LYS-SER-THR

SAH ×2

Metal ions

_ZN ×8

* Residue conservation analysis

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PDB id:

1peg

Name:

Transferase

Title:

Structural basis for the product specificity of histone lysine methyltransferases

Structure:

Histone h3 methyltransferase dim-5. Chain: a, b. Fragment: residues 17-318. Engineered: yes. Histone h3. Chain: p, q. Fragment: residues 1-15. Engineered: yes

Source:

Neurospora crassa. Organism_taxid: 5141. Expressed in: escherichia coli. Expression_system_taxid: 562. (Stratagene). Synthetic: yes. Other_details: the histone h3 peptide (n-terminal residues 1-15) is synthesized.

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: Q8X225 (DIM5_NEUCR)

Seq:

Struc:

Seq:

331 a.a.

Struc:

266 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.2.1.1.43   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N₆-methyl-L-lysine (see diagram below)

Resolution:

2.59Å

R-factor:

0.220

R-free:

0.320

Authors:

X.Zhang,Z.Yang,S.I.Khan,J.R.Horton,H.Tamaru,E.U.Selker, X.Cheng

Key ref:

X.Zhang et al. (2003). Structural basis for the product specificity of histone lysine methyltransferases.. Mol Cell, 12, 177-185. [PubMed id: 12887903] [DOI: 10.1016/S1097-2765(03)00224-7]

Date:

21-May-03

Release date:

05-Aug-03

Related entries:

1ml9
structure of the neurosposa set domain protein dim-5, a
histone h3 lysine methyltrasferase

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Key reference

DOI no: 10.1016/S1097-2765(03)00224-7

Mol Cell 12:177-185 (2003)

PubMed id: 12887903

Structural basis for the product specificity of histone lysine methyltransferases.

X.Zhang, Z.Yang, S.I.Khan, J.R.Horton, H.Tamaru, E.U.Selker, X.Cheng.

ABSTRACT

DIM-5 is a SUV39-type histone H3 Lys9 methyltransferase that is essential for DNA methylation in N. crassa. We report the structure of a ternary complex including DIM-5, S-adenosyl-L-homocysteine, and a substrate H3 peptide. The histone tail inserts as a parallel strand between two DIM-5 strands, completing a hybrid sheet. Three post-SET cysteines coordinate a zinc atom together with Cys242 from the SET signature motif (NHXCXPN) near the active site. Consequently, a narrow channel is formed to accommodate the target Lys9 side chain. The sulfur atom of S-adenosyl-L-homocysteine, where the transferable methyl group is to be attached in S-adenosyl-L-methionine, lies at the opposite end of the channel, approximately 4 A away from the target Lys9 nitrogen. Structural comparison of the active sites of DIM-5, an H3 Lys9 trimethyltransferase, and SET7/9, an H3 Lys4 monomethyltransferase, allowed us to design substitutions in both enzymes that profoundly alter their product specificities without affecting their catalytic activities.

Selected figure(s)

Figure 2.
Figure 2. DIM-5 Kinetics and Ternary Structure(A) Mass spectrometry analysis of different H3 peptides as DIM-5 substrates. The relative amount of each peptide species, expressed as a percentage of the sum of intensity of all related peaks, was plotted over the full time courses of the reactions.(B) GRASP (Nicholls et al., 1991) surface charge distribution (blue for positive, red for negative, white for neutral). The H3 peptide and AdoHcy are shown as stick models.(C) Ribbon (Carson, 1997) diagram colored as in Figure 1. The pre-SET residues (yellow) form a Zn[3]Cys[9] triangular zinc cluster. The SET residues (green) and the N-terminal region are folded into six β sheets surrounding a knot-like structure (magenta). The post-SET residues (gray) bind the fourth zinc atom, adjacent to the substrate H3 peptide (red) and AdoHcy (blue).(D) The substrate H3 peptide (red), superimposed on an omit electron density contoured at 4.0 σ (orange), is inserted as a parallel β strand (red in Figure 2C) between two DIM-5 strands, β10 (green) and β18 (magenta). The side chain density for H3 Arg-8 is complete at lower contour levels (2.5 σ in F[obs]-F[cal] and 0.8 σ in 2F[obs]-F[cal]).

Figure 3.
Figure 3. The Methylation Mechanism(A) The post-SET zinc ion and the AdoHcy binding site. The zinc ion is presented as a red ball, coordinated by four cysteines, C244 (magenta) and C^306XC^308X[4]C^313 (gray). AdoHcy is superimposed onto a difference electron density map contoured at 4.0 σ (orange). Dashed lines indicate the hydrogen bonds. One face of the AdoHcy adenine base lies against the aliphatic portion of R159, whose guanidino group forms a bifurcated salt bridge with the two carboxyl oxygen atoms of E278. The polar edge of the adenine base forms three hydrogen bonds to the DIM-5 backbone: the exocyclic amino group N6 with the carbonyl oxygen of H242, the ring N1 with the amide of L307, and the ring N7 with the amide of H242. The adenine ring carbon C8 makes van der Waals contacts to the Y283 hydroxyl and with the side chain carbonyl Oδ1 of N241; this explains the complete loss of AdoMet crosslinking in N241Q and Y283F mutants (Zhang et al., 2002). The two ribose hydroxyls interact with the main chain amide of V203 and the side chain carboxyl of D202. The amino group of the homocysteine moiety hydrogen bonds the side chain Oδ1 of N241, while its side chain amino group forms two hydrogen bonds with the backbone carbonyl of W161 and with the side chain of E278. The carboxylate group of the homocysteine moiety interacts with Y204 and the backbone amide of W161.(B) Close-up view of the H3 peptide binding site with Lys9 inserted into a channel.(C) The target Lys binding site (stereo). The arrow indicates the movement of the methyl group transferred from the AdoMet methylsulfonium group to the target amino group.(D) DIM-5 activity (LogCPM) as a function of pH.(E) AdoHcy bound in a large surface pocket, allowing for processive methylation. The green ellipse indicates the location where the AdoHcy homocysteine moiety binds in the peptide-free structure (Zhang et al., 2002).

The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 12, 177-185) copyright 2003.

Figures were selected by the author.